BioELX is a retrieve‑rerank framework for cross‑lingual biomedical entity linking that tackles two key problems: the English‑biased UMLS alias training data and the degradation caused by naïvely adding context. It fine‑tunes SapBERT_multi with Wikidata‑derived cross‑lingual alias supervision to create shared concept neighborhoods, and then reranks candidates using pretrained LLMs with mention‑anchored prompting to focus on the target mention. Experiments demonstrate state‑of‑the‑art performance on four benchmarks, improving Recall@1 by 4.8–18.2 percentage points without task‑specific annotations.
By Yi Wang, Corina Dima, Liangyu Zhong, Steffen Staab
arXiv:2608.03154v2 Announce Type: replace
Abstract: Biomedical relation extraction (BioRE) supports knowledge graph construction and hypothesis generation. In real-world settings, most candidate enti...
By Shufan Ming, Yikun Han, Gibong Hong, Rui Zhang, Halil Kilicoglu
TTGBench is a new benchmark for temporal graph learning that evaluates both structural evolution and semantic drift in text‑attributed graphs. It includes six real‑world, text‑rich datasets with dual volatility and supports multi‑class and multi‑label temporal node classification, addressing gaps left by existing benchmarks. A comprehensive evaluation of 17 state‑of‑the‑art methods shows a clear divide: TGNNs excel at structural prediction but struggle with semantic tracking, while LLM‑based models perform better on semantic tasks but lag in structural prediction.
By Longfei Ma, Zemin Liu, Fei Wu
The paper introduces Distilled Rapid Embedding Transfer (DRET), a parameter‑efficient method that injects biomedical domain knowledge from large specialized models into a smaller general‑purpose model without retraining on the original specialized corpora. DRET evolves through iterative strategies—tokenizer‑merge (DRET 1.x), hybrid embedding averaging (DRET 2.0), priority‑based embedding transfer (DRET 3.x), and further refinements (DRET 4.x)—and demonstrates that a 66‑million‑parameter DistilBERT can achieve competitive or superior performance on token‑level PICO classification compared to much larger models, while remaining lightweight. The authors validate the embedding‑level transfer with cosine similarity, semantic‑shift, and t‑SNE analyses, highlighting DRET’s potential for scalable, resource‑efficient biomedical text mining.
By Girish Sundaram, Daniel Berleant
BELXTR is a new biomedical entity linking model that uses a multi‑vector (late interaction) architecture to preserve token‑level matching information, unlike traditional embedding‑based approaches that compress mentions into a single vector. By extending the XTR model with a task‑specific training objective and active query expansion, BELXTR achieves state‑of‑the‑art performance on half of ten evaluated corpora, with an average 5‑percentage‑point gain in recall@1. The model shows especially strong results on cross‑species gene disambiguation, outperforming an LLM‑powered retrieve‑and‑rerank pipeline and approaching a specialized rule‑based system.
By Samuele Garda, Ulf Leser
HERO is a heterogeneous continual graph learning framework that preserves historical knowledge at both structural and semantic levels while adapting to new tasks. It uses DiSCo to select representative target nodes and reconstruct compact heterogeneous contexts, and applies multi-level knowledge distillation to align task-conditioned predictions with semantic responses. Experiments on four datasets with three HGNN backbones show HERO achieves best or tied-best average performance while maintaining competitive forgetting.
By Guiquan Sun, Xikun Zhang, Jingchao Ni, Dongjin Song
arXiv:2609.21387v1 Announce Type: cross
Abstract: Relexicalization is a pivotal technique in clinical NLP, as it facilitates robust masking of sensitive information while synthesizing datasets that r...
By Dipankar Das, Atri Mandal, Sandeep Singh, Tushar Shandhilya
REFINE is a framework that refines medical concept representations by creating patient‑specific temporal graphs from a global text‑attributed knowledge graph. It uses a reinforcement learning policy to allocate a personalized graph expansion budget for each observed code, then processes the resulting graph with a heterogeneous GNN and a frozen LLM that refines representations via graph‑aware soft prompts. Experiments on MIMIC‑III and MIMIC‑IV demonstrate that REFINE consistently improves various EHR prediction backbones, surpasses strong baselines, and shows robust gains across ablation studies, KG selection, and data insufficiency scenarios.
By Mohsen Nayebi Kerdabadi, Arya Hadizadeh Moghaddam, Dongjie Wang, Zijun Yao
arXiv:2606. 15734v1 Announce Type: cross Abstract: Continual post-training enables models to absorb emerging knowledge after deployment, but repeatedly updating shared parameters can accumulate weight drift, potentially causing catastrophic forgetting and degrading general capabilities.
By Weihang Su, Jiacheng Kang, Jingyan Xu, Qingyao Ai, Jianming Long, Hanwen Zhang, Bangde Du, Xinyuan Cao, Min Zhang, Yiqun Liu
EvidenceNet is a disease‑specific dataset that transforms full‑text biomedical literature into structured evidence records and graph representations, preserving study design, provenance, and quantitative support. Using an LLM‑assisted pipeline, it extracts experimentally grounded findings, normalizes entities, scores evidence quality, and links related records via typed semantic relations. The released subsets—EvidenceNet‑HCC and EvidenceNet‑CRC—contain thousands of evidence records and richly connected graphs, with high extraction and relation‑type accuracy, enabling retrieval‑augmented question answering and graph‑based tasks such as link prediction and target prioritization.
By Chang Zong, Jinyu Chen, Sicheng Lv, Si-tu Xue, Huilin Zheng, Jian Wan, Lei Zhang
CohortFlow is a steerable agent for clinical cohort curation that applies natural language corrections as localized updates to a structured specification, allowing selective invalidation of affected computations while keeping valid results. In experiments on 100 clinical‑trial eligibility scenarios, it achieved a micro‑F1 of 77.0% versus 76.4% for full regeneration, a non‑significant difference, but reduced correction latency by 64.8% after completion and 44.3% during execution, and cut model calls by 38.1%. A proof‑of‑concept run on MIMIC showed all 13 cohort states executed successfully, with corrections preserving unaffected computations and recomputing only changed or dependent nodes.
By Neil Chen, Adrian Serapio, Hanxue Gu, Evan Lee, Kang Wang, Yang Yang
EHRAdapt is an adapter that maps electronic health record tuples directly into a frozen language model’s embedding space, using learned embeddings for modality, time gaps, and dedicated vectors for event codes. It represents each event vector as a sum of a frozen, ontology‑trained semantic prior and a low‑rank evidence residual, enabling robust learning even for rare clinical events. Experiments on four million patient records with three large language model backbones show that the full adapter outperforms all ablations in next‑event prediction and improves rare‑disease discrimination in classification tasks.
By Andre R Goncalves, Vincent Liu, Priyadip Ray